Changing a fasta header

Hi I have a fasta file anotated and I want to add to the first position after > the next word to 'Similar to'

   >_Anouracaudifer_00017283-RA transcript Name:"Similar to Chid1 Chitinase domain-containing protein 1 (Rattus norvegicus OX=10116)" offset:0 AED:0.30 eAED:0.30 QI:0|0|0|1|1|1|12|0|393
ATGAAGGCGCTCCTGCATGTGCTCTGGCTCACTCTGGCCTGCGGCTCTGCTCACACCACCCTGTCGAAGTCGGATGCCAAGAAGTCTGCCTCCAAGACACTGCAGGAGAAGACTCAGCTCTCAGAGACACCTGTGCAGGACCGGGGTCTGGTGGTAACAGACCCCCGAGCCGAGGACG

I want the output to be like this

>Chid1_Anouracaudifer_00017283-RA transcript Name:"Similar to Chid1 Chitinase domain-containing protein 1 (Rattus norvegicus OX=10116)" offset:0 AED:0.30 eAED:0.30 QI:0|0|0|1|1|1|12|0|393
ATGAAGGCGCTCCTGCATGTGCTCTGGCTCACTCTGGCCTGCGGCTCTGCTCACACCACCCTGTCGAAGTCGGATGCCAAGAAGTCTGCCTCCAAGACACTGCAGGAGAAGACTCAGCTCTCAGAGACACCTGTGCAGGACCGGGGTCTGGTGGTAACAGACCCCCGAGCCGAGGACG

How can i do it? i already tried with

sed -E 's/(Similar to )(\w+)/>CHIA_\2\1\2/' file.txt > new_file_2.txt

and store it in a new file and tried to paste it into the headers but it does not work , any ideas?

fasta changingheader preprocessing header

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updated 3.3 years ago by rpolicastro

• written 3.3 years ago by Diana Nadia •

2 answers

Your sed idea was close, here's a working implementation.

sed -E 's/(^>)(.+Similar to )(\S+)(.+)/\1\3\2\3\4/' in.fasta

You can take a similar approach with seqkit too, which I tend to prefer for fasta manipulation.

seqkit replace -p "(.+Similar to )(\S+)(.+)" -r "\$2\$1\$2\$3" in.fasta

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written 3.3 years ago by rpolicastro

I like to use bioawk to edit fasta files.

>_Anouracaudifer_00017283-RA transcript Name:"Similar to Chid1 Chitinase domain-containing protein 1 (Rattus norvegicus OX=10116)" offset:0 AED:0.30 eAED:0.30 QI:0|0|0|1|1|1|12|0|393
ATGAAGGCGCTCCTGCATGTGCTCTGGCTCACTCTGGCCTGCGGCTCTGCTCACACCACCCTGTCGAAGTCGG

bioawk -c fastx '{a=match($4,"Similar to");b=substr($4,a+11,5);print ">"b$name" "$4"\n"$seq}' test.fa

>Chid1_Anouracaudifer_00017283-RA transcript Name:"Similar to Chid1 Chitinase domain-containing protein 1 (Rattus norvegicus OX=10116)" offset:0 AED:0.30 eAED:0.30 QI:0|0|0|1|1|1|12|0|393
ATGAAGGCGCTCCTGCATGTGCTCTGGCTCACTCTGGCCTGCGGCTCTGCTCACACCACCCTGTCGAAGTCGG

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written 3.3 years ago by YiweiZhu •